Cannot Pull b/c "You have unstaged changes", but status says there are no changes

Instead of

git pull

try

git fetch
git rebase -p origin/master

If that doesn't work you can try

git pull --no-rebase

How to check why this message occurs

Make sure you on a branch, not a detached head. Rebasing doesn't work on a detached head.

Run the following commands, the result should be no output.

git update-index -q --ignore-submodules --refresh
git diff-files --ignore-submodules
git diff-index --cached --ignore-submodules HEAD --

Are you working on local filesystem or nfs share?

I had exactly the same problem when I was working on nfs share.

I have added noatime option to the mount command and it helped:

mount -t nfs -o noatime,... device dir